Cotton Genomics and Genetics 2024, Vol.15, No.2, 103-111 http://cropscipublisher.com/index.php/cgg 105 Marker-Assisted Selection (MAS): The identification of quantitative trait loci (QTLs) and candidate genes associated with important traits, such as photoperiod insensitivity, has enabled the use of DNA markers in MAS. This approach accelerates the breeding process by allowing the selection of desirable traits at the molecular level (Kushanov et al., 2022). These advancements highlight the critical role of cytogenetic markers in enhancing the efficiency and precision of Gossypiumbreeding programs, ultimately contributing to the development of superior cotton varieties. 3 Cytogenetic Markers inGossypium 3.1 Chromosomal structure and karyotyping inGossypium Chromosomal structure and karyotyping are fundamental in understanding the genetic makeup and diversity within Gossypiumspecies. Karyotyping involves the examination of chromosome number and structure, which is crucial for identifying genetic variations and abnormalities. For instance, the study of early-maturing upland cotton (Gossypium hirsutum L.) using Simple Sequence Repeat (SSR) markers revealed significant polymorphisms and genetic diversity among different cultivars, which is essential for breeding programs aimed at improving cotton varieties (Kuang et al., 2022). Additionally, the use of cytogenetic markers such as 18S and 5S rDNA genes has been instrumental in characterizing hybrids and understanding karyotypic diversity in other species, which can be applied to Gossypiumas well (Goes et al., 2020). 3.2 Fluorescent in situ hybridization (FISH) in cotton Fluorescent In Situ Hybridization (FISH) is a powerful technique used to identify specific chromosomes and their rearrangements. This method has been successfully applied in various species to study karyotype evolution and chromosomal organization. For example, FISH has been used to identify and map the distribution of histone H3 genes in Lepidoptera, providing insights into the stable organization of genomes (Provazníková et al., 2021). In Gossypium, FISH can be utilized to map important genetic markers and understand chromosomal behavior during hybridization and breeding processes. The application of FISH in cotton breeding programs can enhance the identification of desirable traits and accelerate the development of improved cotton varieties. 3.3 Use of molecular cytogenetics in cotton genome mapping Molecular cytogenetics involves the use of molecular markers to map the genome and identify quantitative trait loci (QTL) associated with important agronomic traits. In cotton, various molecular markers such as RFLP, AFLP, RAPD, SSR, EST-SSR, and SNP have been employed to map genes controlling traits like fiber quality, drought tolerance, and yield (Shukla et al., 2021). The identification of tightly linked molecular markers with high predictive trait values is crucial for successful QTL analysis and breeding programs. For instance, SSR markers have been used to explore genetic diversity and perform DNA fingerprinting in Gossypium hirsutum, providing valuable information for future breeding efforts (Kuang et al., 2022). The integration of molecular cytogenetics in cotton genome mapping facilitates the precise identification of genetic loci and accelerates the breeding of superior cotton varieties. 4 Applications of Cytogenetic Markers inGossypiumBreeding 4.1 Genetic diversity and germplasm characterization Cytogenetic markers play a crucial role in assessing genetic diversity and characterizing germplasm in Gossypium species. By utilizing these markers, researchers can identify and catalog the genetic variations present within and between different cotton species. This information is vital for the conservation of genetic resources and for the selection of parent lines in breeding programs. For instance, the study by (Kushanov et al., 2021) highlights the use of molecular markers to explore the genetic diversity within the Gossypiumgenus, which aids in the creation of high-yielding cultivars with superior fiber quality and stress adaptation (Figure 1). Kushanov et al. (2021) compares conventional breeding with marker-assisted selection (MAS). Conventional breeding relies on phenotypic selection, which is challenging to automate, cannot distinguish between heterozygotes and dominant homozygotes, and is influenced by environmental factors. MAS, on the other hand, utilizes genotypic selection through DNA markers, enabling almost complete automation, accurate identification
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